// not used for now april 9 2012
int removevariants(struct fragment* Flist,int fragments,struct SNPfrags* snpfrag,int snps,int maxiter,char* HAP1,char* HAP2,struct BLOCK* clist,int components)
{
int iter=0,k=0;
float calls=0, miscalls=0,ll=0, bestll =0;
//int switches =0; int prev = 0;
/*****************************************************************************************************/
//for (i=0;i<snps;i++) fprintf(stdout,"first fragment for SNP %d %d \n",i,snpfrag[i].ff);
mecscore(Flist,fragments,HAP1,&ll,&calls,&miscalls); bestll = ll;
for (iter =0; iter < 1;iter++)
{
fprintf(stdout,"MEC score %f %f LL %f bestLL %f \n",miscalls,calls,ll,bestll);
fprintf(stderr,"MEC score %f %f LL %f bestLL %f\n",miscalls,calls,ll,bestll);
for (k=0;k<components;k++) find_bestvariant_segment(Flist,fragments,snpfrag,clist,k,HAP1,HAP2);
//mecscore(Flist,fragments,HAP1,&ll,&calls,&miscalls); if (bestll > ll) bestll = ll;
}
return 1;
}
int maxcut_haplotyping(char* fragmentfile,char* variantfile,int snps,char* outputfile,int maxiter_hapcut)
{
// IMP NOTE: all SNPs start from 1 instead of 0 and all offsets are 1+
fprintf(stderr,"calling MAXCUT based haplotype assembly algorithm\n");
int fragments=0,iter=0,components=0; int i=0,j=0,k=0,t=0,component; int* slist; int flag =0;
float bestscore_mec = 0,calls=0, miscalls=0,ll = 0;
char buffer[MAXBUF];
/****************************** READ FRAGMENT MATRIX*************************************************/
struct fragment* Flist; FILE* ff = fopen(fragmentfile,"r");
if (ff == NULL) { fprintf(stderr,"couldn't open fragment file %s\n",fragmentfile); exit(0);}
fragments =0; while ( fgets(buffer,MAXBUF,ff) != NULL) fragments++; fclose(ff);
Flist = (struct fragment*)malloc(sizeof(struct fragment)*fragments);
flag = read_fragment_matrix(fragmentfile,Flist,fragments);
if (flag < 0) { fprintf(stderr,"unable to read fragment matrix file %s \n",fragmentfile); return -1; }
if (VCFformat ==0) snps = count_variants(variantfile);
else snps = count_variants_vcf(variantfile);
if (snps < 0) { fprintf(stderr,"unable to read variant file %s \n",variantfile); return -1; }
fprintf(stderr,"processed fragment file and variant file: fragments %d variants %d\n",fragments,snps);
/****************************** READ FRAGMENT MATRIX*************************************************/
struct SNPfrags* snpfrag = (struct SNPfrags*)malloc(sizeof(struct SNPfrags)*snps);
update_snpfrags(Flist,fragments,snpfrag,snps,&components);
double MEM_ALLOC = 0; for (i=0;i<snps;i++) MEM_ALLOC += snpfrag[i].edges*0.002; MEM_ALLOC *= 0.016;
fprintf(stderr,"%f MB memory needs to be allocated for graph edges\n",MEM_ALLOC); // size of struct edge is 16/1000 bytes
if (MEM_ALLOC >= MAX_MEMORY)
{
fprintf(stderr,"\nstoring the HAPCUT graph structure requires more than %d MB of memory:\n 1. increase the maximum memory available using option \"--maxmem 12000\" where the memory is specified in megabytes OR \n 2. run the program with the options \"--longreads 1 \" to reduce the number of edges stored \n\n",MAX_MEMORY);
return -1;
}
// too much memory allocated here for fosmid based data...
for (i=0;i<snps;i++) snpfrag[i].elist = (struct edge*)malloc(sizeof(struct edge)*snpfrag[i].edges);
for (i=0;i<snps;i++) snpfrag[i].telist = (struct edge*)malloc(sizeof(struct edge)*snpfrag[i].edges);
if (FOSMIDS ==0) add_edges(Flist,fragments,snpfrag,snps,&components);
else if (FOSMIDS >=1) add_edges_fosmids(Flist,fragments,snpfrag,snps,&components);
// this considers only components with at least two nodes
fprintf(stderr,"fragments %d snps %d component(blocks) %d\n",fragments,snps,components);
struct BLOCK* clist = (struct BLOCK*)malloc(sizeof(struct BLOCK)*components); component =0;
generate_clist_structure(Flist,fragments,snpfrag,snps,components,clist);
/*****************************************************************************************************/
char* HAP1 = (char*)malloc(snps+1); char* besthap_mec = (char*)malloc(snps+1);
char* HAP2 = (char*)malloc(snps+1);
struct tm *ts1; char buf[80]; time_t now;
slist = (int*)malloc(sizeof(int)*snps); char fn[1000];
if (VCFformat ==0) read_variantfile(variantfile,snpfrag,snps); else read_vcffile(variantfile,snpfrag,snps);
/*****************************************************************************************************/
if (RANDOM_START ==1)
{
fprintf(stdout,"starting from a completely random solution SOLUTION \n");
for (i=0;i<snps;i++)
{
if (snpfrag[i].frags ==0) { HAP1[i] = '-'; HAP2[i] = '-'; }
else
{
if (drand48() < 0.5) { HAP1[i] = '0'; HAP2[i] = '1'; } else {HAP1[i] = '1'; HAP2[i] = '0'; }
}
}
}
for (i=0;i<snps;i++) { besthap_mec[i] = HAP1[i]; }
// for each block, we maintain best haplotype solution under MFR criterion
// compute the component-wise score for 'initHAP' haplotype
miscalls=0;bestscore_mec=0;
for (k=0;k<components;k++)
{
clist[k].MEC =0; clist[k].bestMEC =0; clist[k].calls =0; clist[k].LL = 0;
for (i=0;i<clist[k].frags;i++)
{
update_fragscore(Flist,clist[k].flist[i],HAP1); clist[k].MEC += Flist[clist[k].flist[i]].currscore;
clist[k].LL += Flist[clist[k].flist[i]].ll; clist[k].calls += Flist[clist[k].flist[i]].calls;
}
clist[k].bestMEC = clist[k].MEC; bestscore_mec += clist[k].bestMEC; miscalls += clist[k].MEC; clist[k].bestLL = clist[k].LL;
}
// annealing_haplotyping(Flist,fragments,snpfrag,snps,maxiter,HAP1,HAP2,clist,components,slist); return 1;
// annealing_haplotyping_full(Flist,fragments,snpfrag,snps,maxiter,HAP1,HAP2,0); return 1;
/************************** RUN THE MAX_CUT ALGORITHM ITERATIVELY TO IMPROVE MEC SCORE*********************************/
for (iter=0;iter<maxiter_hapcut;iter++)
{
mecscore(Flist,fragments,HAP1,&ll,&calls,&miscalls);
time(&now); ts1 = localtime(&now); strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts1);
fprintf(stdout,"iter %d current haplotype MEC %f calls %d LL %f %s \n",iter,miscalls,(int)calls,ll,buf);
fprintf(stderr,"iter %d current haplotype MEC %f calls %d LL %f %s \n",iter,miscalls,(int)calls,ll,buf);
if ((iter%10==0 && iter > 0))
{
// new code added april 7 2012
for (k=0;k<components;k++) find_bestvariant_segment(Flist,fragments,snpfrag,clist,k,HAP1,HAP2);
sprintf(fn,"%s",outputfile); // newfile for every update to score....
//sprintf(fn,"%s.%f",outputfile,miscalls); // newfile for every update to score....
fprintf(stdout,"OUTPUTTING HAPLOTYPE ASSEMBLY TO FILE %s\n",fn); fprintf(stderr,"OUTPUTTING HAPLOTYPE ASSEMBLY TO FILE %s\n",fn);
//if (VCFformat ==1) print_haplotypes_vcf(clist,components,HAP1,Flist,fragments,snpfrag,snps,fn);
print_hapfile(clist,components,HAP1,Flist,fragments,snpfrag,variantfile,miscalls,fn);
// do this only if some option is specified
if (PRINT_FRAGMENT_SCORES ==1)
{
print_fragmentmatrix_MEC(Flist,fragments,HAP1,outputfile);
//print_matrix(clist,components,HAP1,Flist,outputfile);
}
}
for (k=0;k<components;k++) // COMPUTATION OF TREE FOR EACH COMPONENT
{
//if ((k*50)%components ==0) fprintf(stderr,"#");
if (iter ==0) fprintf(stdout,"\n component %d length %d phased %d %d...%d \n",k,clist[k].length,clist[k].phased,clist[k].offset,clist[k].lastvar);
// call function for each component only if MEC > 0 april 17 2012
if (clist[k].MEC > 0) evaluate_cut_component(Flist,snpfrag,clist,k,slist,HAP1,iter);
}
for (i=0;i<snps;i++)
{
// commented out on april 6 4pm 2012
//if (HAP1[i] == '0') HAP2[i] = '1'; else if (HAP1[i] == '1') HAP2[i] = '0'; else HAP2[i] = HAP1[i];
}
}
/************************** RUN THE MAX_CUT ALGORITHM ITERATIVELY TO IMPROVE MEC SCORE*********************************/
// annealing_haplotyping_full(Flist,fragments,snpfrag,snps,maxiter+100,HAP1,HAP2,0); return 1;
return 1;
}
